Variant report

Variant	rs1320149
Chromosome Location	chr2:97493877-97493878
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:97493359-97495013	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:97493300-97494915	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr2:97493467-97493977	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:97493401-97493905	HepG2	liver:	n/a	n/a
5	POLR2A	chr2:97493347-97494834	K562	blood:	n/a	n/a
6	POLR2A	chr2:97493340-97494365	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:97492698..97495238-chr2:97505220..97508779,3	MCF-7	breast:
2	chr2:97492185..97494409-chr2:97534790..97536451,2	MCF-7	breast:
3	chr2:97489114..97491853-chr2:97492088..97494709,3	K562	blood:

Variant related genes	Relation type
CNNM3	TF binding region
ENSG00000163126	Chromatin interaction
ENSG00000168758	Chromatin interaction
ENSG00000168763	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10439526	0.81[EUR][1000 genomes]
rs11897786	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12846	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1317911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1320146	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs13419073	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17119598	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs2276654	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs4077343	0.80[EUR][1000 genomes]
rs55674661	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58147284	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62152790	0.80[EUR][1000 genomes]
rs62152793	0.84[EUR][1000 genomes]
rs62152794	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62152795	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62152834	0.81[EUR][1000 genomes]
rs6576986	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs6576987	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs6576989	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6753987	0.83[AMR][1000 genomes]
rs72811623	0.80[EUR][1000 genomes]
rs7580942	0.84[EUR][1000 genomes]
rs7594727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7608621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9948	0.87[CEU][hapmap]
rs9973492	0.88[CEU][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv874681	chr2:97410949-97577343	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
10	nsv874682	chr2:97423626-97567389	Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
11	nsv1009720	chr2:97464803-97522856	Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
12	nsv535830	chr2:97464803-97522856	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1320149	FAHD2CP	cis	Muscle Skeletal	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97483600-97498200	Weak transcription	HSMM	muscle
2	chr2:97483800-97494400	Weak transcription	Osteobl	bone
3	chr2:97483800-97498400	Weak transcription	NHDF-Ad	bronchial
4	chr2:97484600-97518400	Weak transcription	HUVEC	blood vessel
5	chr2:97485200-97498400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:97486000-97505000	Strong transcription	Fetal Stomach	stomach
7	chr2:97486600-97498000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:97486800-97500800	Strong transcription	Thymus	Thymus
9	chr2:97487000-97498800	Strong transcription	Primary B cells from peripheral blood	blood
10	chr2:97487200-97501800	Strong transcription	Primary T cells from cord blood	blood
11	chr2:97487200-97504000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:97487400-97499200	Weak transcription	Fetal Brain Male	brain
13	chr2:97487400-97501800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:97487400-97504200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:97487600-97504600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr2:97488000-97497400	Strong transcription	Spleen	Spleen
17	chr2:97488000-97498200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:97488000-97499000	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr2:97488000-97501200	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr2:97488200-97497000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr2:97488200-97497400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr2:97488200-97497400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:97488200-97497400	Strong transcription	Placenta	Placenta
24	chr2:97488200-97497600	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr2:97488200-97497600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:97488200-97499200	Strong transcription	Brain Germinal Matrix	brain
27	chr2:97488200-97499600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr2:97488200-97501200	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr2:97488200-97501800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr2:97488400-97497800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr2:97488400-97499200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr2:97488400-97499400	Strong transcription	Brain Substantia Nigra	brain
33	chr2:97488400-97499600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr2:97488400-97501200	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr2:97488600-97497400	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr2:97488600-97497800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr2:97488600-97497800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:97488600-97498000	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr2:97488600-97499200	Strong transcription	Aorta	Aorta
40	chr2:97488600-97499400	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr2:97488600-97501200	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr2:97488600-97504600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr2:97488800-97499400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr2:97488800-97501600	Strong transcription	Brain Angular Gyrus	brain
45	chr2:97489000-97497400	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr2:97489000-97499000	Strong transcription	Colonic Mucosa	Colon
47	chr2:97489200-97497800	Weak transcription	Right Atrium	heart
48	chr2:97489200-97501400	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr2:97489400-97497400	Strong transcription	Adipose Nuclei	Adipose
50	chr2:97489400-97501200	Strong transcription	Primary T helper cells fromperipheralblood	blood

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